SOP (Standard Operating Procedure )

Using an Electrophoresis System/ Gel Box

1. If the electrophoresis chamber (gel box) has a lid on it, remove the lid. Note how the lid makes contact on the box you are using.The lid is usually removed by sliding it backwards off the box. (Some chambers may have lid held with magnetic contacts so that lid lifts up and off.)

2. Place the agarose gel (sitting in a casting tray or not) in the center of the chamber. “Wells” in the gel ALWAYS go at black (negative) end. *Remember Run to Red* is the direction you want your sample to move. (If running dyes, you may have wells in the middle of the gel so the dyes can run in either direction.)

3. Add buffer (type indicated by lab) to one side of the chamber until it is level with the top of the gel. Next add buffer to the other side. Stop filling when buffer is 2mm above the top of the gel. Be careful not to overfill. (Too much buffer will allow the current to flow over the gel rather than through the gel, and will slow down the movement of your sample through the gel.)

3. Using appropriate pipettor, load samples into the wells. Hold the pipettor just above the well to release the sample. The sample is prepared with sugar or glycerol so that it sinks into the well. Do not put the pipettor tip INTO the well because you may puncture the well and your sample will leak out through the bottom of the gel. ALWAYS change pipette tips for each sample.

4. A. Usually contacts are on the side of the box so you will slide the lid onto the chamber. Red matches with (+) sign and black with (-) sign.

4. B. If contacts are magnetic, you will just set the lid onto the top of the box, matching colors: red to red, black to black. Be sure the wires are fed through the openings.

5. Plug leads into power source. Black cord= black hole, red cord=red hole. (Some power sources can run 2 boxes, others can run 4 boxes.)

6. Plug power source into wall socket. Set voltage to either 125V or 70V. Check with your instructor or check your protocol. Turn power “on”.

7. Now make sure that it’s running properly. You should see bubbles rising at the bottom of each side of the chamber. If not, turn off and reset all the connections and try again.

8. Run the gel for the appropriate amount of time as determined by the progress of the tracking dye or by your teacher or the protocol.

9. When the run is complete, turn the power supply off, disconnect the leads from the chamber to the power supply, and finally carefully remove the lid from chamber to retrieve your gel for visualization or staining.

10. To "clean" the electrophoresis chamber, rinse it thoroughly first with tap water, then with distilled water. Then let it AIR DRY. Do not attempt to dry it with paper towels because you might damage the thin wires on the bottom of the chamber sides.